Is there a good way to clean up the schratches on the rub rail? Someone told me you can sand them out but won't that dull the black rubber. Just wanted to know if anyone had any other ideas or exactly what grit of sandpaper to use.

Rubber ? Most of the rubrails are a plastic material. Your course of action will be greatly different for rubber.

If it is is plastic you can try Brasso or any mild abrasive to smooth out scratches. You can also replace the insert relatively easily, I did this over the winter and it makes a big difference to the overall look of the boat...check out this site: